This file is indexed.

/usr/share/emacs/site-lisp/ess/ess-r-completion.el is in ess 17.11-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
;;; ess-r-completion.el --- R completion
;;
;; Copyright (C) 2015 A.J. Rossini, Richard M. Heiberger, Martin Maechler, Kurt
;;      Hornik, Rodney Sparapani, Stephen Eglen and Vitalie Spinu.
;;
;; Author: Vitalie Spinu
;; Maintainer: ESS-core <ESS-core@r-project.org>
;;
;; Keywords: languages, statistics
;;
;; This file is part of ESS.
;;
;; This file is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 2, or (at your option)
;; any later version.
;;
;; This file is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; A copy of the GNU General Public License is available at
;; http://www.r-project.org/Licenses/
;;
;;; Commentary:
;;
;;; Code:


;;; ElDoc

(require 'cl)
(require 'ess-utils)

(defun ess-r-eldoc-function ()
  "Return the doc string, or nil.
If an ESS process is not associated with the buffer, do not try
to look up any doc strings."
  (interactive)
  (when (and eldoc-mode ess-can-eval-in-background)
    (let* ((proc (ess-get-next-available-process))
           (funname (and proc (or (and ess-eldoc-show-on-symbol ;; Aggressive completion
                                       (thing-at-point 'symbol))
                                  (car (ess--funname.start))))))
      (when funname
        (let* ((args (ess-function-arguments funname proc))
               (bargs (cadr args))
               (doc (mapconcat (lambda (el)
                                 (if (equal (car el) "...")
                                     "..."
                                   (concat (car el) "=" (cdr el))))
                               bargs ", "))
               (margs (nth 2 args))
               (W (- (window-width (minibuffer-window)) (+ 4 (length funname))))
               doc1)
          (when doc
            (setq doc (ess-eldoc-docstring-format funname doc))
            (when (and margs (< (length doc1) W))
              (setq doc1 (concat doc (propertize "  || " 'face font-lock-function-name-face)))
              (while (and margs (< (length doc1) W))
                (let ((head (pop margs)))
                  (unless (assoc head bargs)
                    (setq doc doc1
                          doc1 (concat doc1 head  "=, ")))))
              (when (equal (substring doc -2) ", ")
                (setq doc (substring doc 0 -2)))
              (when (and margs (< (length doc) W))
                (setq doc (concat doc " {--}"))))
            doc))))))

(defun ess-eldoc-docstring-format (funname doc)
  (save-match-data
    (let* (;; (name (symbol-name sym))
           (truncate (or  (not (eq t eldoc-echo-area-use-multiline-p))
                          (eq ess-eldoc-abbreviation-style 'aggressive)))
           ;; Subtract 1 from window width since will cause a wraparound and
           ;; resize of the echo area.
           (W (1- (- (window-width (minibuffer-window))
                     (+ 2 (length funname)))))
           newdoc)
      (setq doc
            (if (or (<= (length doc) W)
                    (null ess-eldoc-abbreviation-style)
                    (eq 'none ess-eldoc-abbreviation-style))
                doc
              ;;MILD filter
              (setq doc (replace-regexp-in-string "TRUE" "T" doc))
              (setq doc (replace-regexp-in-string "FALSE" "F" doc))
              (if (or (<= (length doc) W)
                      (eq 'mild ess-eldoc-abbreviation-style))
                  doc
                ;;NORMAL filter (deal with long defaults)
                (setq doc (replace-regexp-in-string
                           ;; function calls inside default docs foo(xxxx{..})
                           "([^)]\\{8\\}\\([^)]\\{4,\\}\\))"
                           "{.}" doc nil nil 1))
                (if (<= (length doc) W)
                    doc
                  (setq doc (replace-regexp-in-string
                             " +[^ \t=,\"\]+=[^ \t]\\{10\\}\\([^ \t]\\{4,\\}\\)\\(,\\|\\'\\)"
                             "{.}," doc nil nil 1))
                  (if (<= (length doc) W)
                      doc
                    (setq doc (replace-regexp-in-string
                               " +[^ \t=,\"]+=\\([^ \t]\\{10,\\}\\)\\(,\\|\\'\\)"
                               "{.}," doc nil nil 1))
                    (if (or (<= (length doc) W)
                            (eq 'normal ess-eldoc-abbreviation-style))
                        doc
                      ;;STRONG filter (replace defaults)
                      (setq doc (replace-regexp-in-string
                                 " *[^ \t=,\"\\]* = \\([^ \t]\\{4,\\}\\)\\(,\\|\\'\\)"
                                 "{.}," doc nil nil 1))
                      (if (<= (length doc) W)
                          doc
                        (setq doc (replace-regexp-in-string
                                   "\\(=[^FT0-9].+?\\)\\(, [^ =,\"\\]+=\\|\\'\\)"
                                   "" doc nil nil 1))
                        (setq doc (replace-regexp-in-string
                                   "\\(=[^FT0-9].+?\\)\\(, [^ =,\"\\]+,\\|\\'\\)"
                                   "" doc nil nil 1))
                        (if (or (<= (length doc) W)
                                (eq 'strong ess-eldoc-abbreviation-style))
                            doc
                          ;;AGGRESSIVE filter (truncate what is left)
                          (concat (substring doc 0 (- W 4)) "{--}")))))))))
      (when (and truncate
                 (> (length doc) W))
        (setq doc (concat (substring doc 0 (- W 4)) "{--}")))
      (format "%s: %s" (propertize funname 'face 'font-lock-function-name-face) doc))))


;;; OBJECTS

(defun ess-r-object-completion ()
  "Return completions at point in a format required by `completion-at-point-functions'."
  (if (ess-make-buffer-current)
      (let* ((funstart (cdr (ess--funname.start)))
             (completions (ess-r-get-rcompletions funstart))
             (token (pop completions)))
        (when completions
          (list (- (point) (length token)) (point)
                completions)))
    (when (string-match "complete" (symbol-name last-command))
      (message "No ESS process associated with current buffer")
      nil)))

(defun ess-complete-object-name ()
  "Perform completion on `ess-language' object preceding point.
Uses \\[ess-r-complete-object-name] when `ess-use-R-completion' is non-nil,
or \\[ess-internal-complete-object-name] otherwise."
  (interactive)
  (if (ess-make-buffer-current)
      (if ess-use-R-completion
          (ess-r-complete-object-name)
        (ess-internal-complete-object-name))
    ;; else give a message on second invocation
    (when (string-match "complete" (symbol-name last-command))
      (message "No ESS process associated with current buffer")
      nil)))

(defun ess-complete-object-name-deprecated ()
  "Gives a deprecated message "
  (interactive)
  (ess-complete-object-name)
  (message "C-c TAB is deprecated, completions has been moved to [M-TAB] (aka C-M-i)")
  (sit-for 2 t))

;; This one is needed for R <= 2.6.x -- hence *not* obsoleting it
(defun ess-internal-complete-object-name ()
  "Perform completion on `ess-language' object preceding point.
The object is compared against those objects known by
`ess-get-object-list' and any additional characters up to ambiguity are
inserted.  Completion only works on globally-known objects (including
elements of attached data frames), and thus is most suitable for
interactive command-line entry, and not so much for function editing
since local objects (e.g. argument names) aren't known.

Use \\[ess-resynch] to re-read the names of the attached directories.
This is done automatically (and transparently) if a directory is
modified (S only!), so the most up-to-date list of object names is always
available.  However attached dataframes are *not* updated, so this
command may be necessary if you modify an attached dataframe."
  (interactive)
  (ess-make-buffer-current)
  (if (memq (char-syntax (preceding-char)) '(?w ?_))
      (let* ((comint-completion-addsuffix nil)
             (end (point))
             (buffer-syntax (syntax-table))
             (beg (unwind-protect
                      (save-excursion
                        (set-syntax-table ess-mode-syntax-table)
                        (backward-sexp 1)
                        (point))
                    (set-syntax-table buffer-syntax)))
             (full-prefix (buffer-substring beg end))
             (pattern full-prefix)
             ;; See if we're indexing a list with `$'
             (listname (if (string-match "\\(.+\\)\\$\\(\\(\\sw\\|\\s_\\)*\\)$"
                                         full-prefix)
                           (progn
                             (setq pattern
                                   (if (not (match-beginning 2)) ""
                                     (substring full-prefix
                                                (match-beginning 2)
                                                (match-end 2))))
                             (substring full-prefix (match-beginning 1)
                                        (match-end 1)))))
             ;; are we trying to get a slot via `@' ?
             (classname (if (string-match "\\(.+\\)@\\(\\(\\sw\\|\\s_\\)*\\)$"
                                          full-prefix)
                            (progn
                              (setq pattern
                                    (if (not (match-beginning 2)) ""
                                      (substring full-prefix
                                                 (match-beginning 2)
                                                 (match-end 2))))
                              (ess-write-to-dribble-buffer
                               (format "(ess-C-O-Name : slots..) : patt=%s"
                                       pattern))
                              (substring full-prefix (match-beginning 1)
                                         (match-end 1)))))
             (components (if listname
                             (ess-object-names listname)
                           (if classname
                               (ess-slot-names classname)
                             ;; Default case: It hangs here when
                             ;;    options(error=recover) :
                             (ess-get-object-list ess-current-process-name)))))
        ;; always return a non-nil value to prevent history expansions
        (or (comint-dynamic-simple-complete  pattern components) 'none))))

(defun ess-r-get-rcompletions (&optional start end prefix allow-3-dots)
  "Call R internal completion utilities (rcomp) for possible completions.
Optional START and END delimit the entity to complete, default to
bol and point.  If PREFIX is given, perform completion on
PREFIX.  First element of the returned list is the completion
token.  Needs version of R >= 2.7.0."
  (let* ((start (or start
                    (if prefix
                        0
                      (save-excursion (comint-bol nil) (point)))))
         (end (or end (if prefix (length prefix) (point))))
         (prefix (or prefix (buffer-substring start end)))
         ;; (opts1 (if no-args "op<-rc.options(args=FALSE)" ""))
         ;; (opts2 (if no-args "rc.options(op)" ""))
         (call1 (format ".ess_get_completions(\"%s\", %d)"
                        (ess-quote-special-chars prefix)
                        (- end start)))
         (cmd (if allow-3-dots
                  (concat call1 "\n")
                (concat "local({ r <- " call1 "; r[r != '...='] })\n"))))

    (ess-get-words-from-vector cmd)))

(defun ess-r-complete-object-name ()
  "Completion in R via R's completion utilities (formerly 'rcompgen').
To be used instead of ESS' completion engine for R versions >= 2.7.0."
  (interactive)
  (let ((possible-completions (ess-r-get-rcompletions))
        token-string)
    ;; If there are no possible-completions, should return nil, so
    ;; that when this function is called from
    ;; comint-dynamic-complete-functions, other functions can also be
    ;; tried.
    (when possible-completions
      (setq token-string (pop possible-completions))
      (or (comint-dynamic-simple-complete token-string
                                          possible-completions)
          'none))))

(defvar ess--cached-sp-objects nil)

(defun ess--get-cached-completions (prefix &optional point)
  (if (string-match-p "[]:$@[]" prefix)
      ;; call proc for objects
      (cdr (ess-r-get-rcompletions nil nil prefix))
    ;; else, get cached list of objects
    (with-ess-process-buffer 'no-error ;; use proc buf alist
      (ess-when-new-input last-cached-completions
        (if (and ess--cached-sp-objects
                 (not  (process-get *proc* 'sp-for-ac-changed?)))
            ;; if global cache is already there, only re-read local .GlobalEnv
            (progn
              (unless ess-sl-modtime-alist
                ;; initialize if empty
                (setq ess-sl-modtime-alist '((".GlobalEnv" nil))))
              ;; fixme: Make adaptive. Not on all remotes are slow; For lots of
              ;; objects in .GlobalEnv,locals could also be slow.
              (unless (file-remote-p default-directory)
                (ess-extract-onames-from-alist ess-sl-modtime-alist 1 'force)))
          (if ess--cached-sp-objects
              (ess-get-modtime-list 'ess--cached-sp-objects 'exclude-first)
            (ess-get-modtime-list)
            (setq ess--cached-sp-objects (cdr ess-sl-modtime-alist)))
          ;; reread new package, but not rda, much faster and not needed anyways
          (process-put *proc* 'sp-for-ac-changed? nil)))
      (apply 'append
             (cddar ess-sl-modtime-alist) ; .GlobalEnv
             (mapcar 'cddr ess--cached-sp-objects)))))


;;; ARGUMENTS

(defcustom ess-R-argument-suffix " = "
  "Suffix appended by `ac-source-R' and `ac-source-R-args' to candidates."
  :group 'R
  :type 'string)

(define-obsolete-variable-alias 'ess-ac-R-argument-suffix 'ess-R-argument-suffix "15.3")

(defvar ess-r--funargs-pre-cache
  '(("plot"
     (("graphics")
      (("x" . "")    ("y" . "NULL")    ("type" . "p")    ("xlim" . "NULL")    ("ylim" . "NULL")    ("log" . "")    ("main" . "NULL")    ("sub" . "NULL")    ("xlab" . "NULL")    ("ylab" . "NULL")
       ("ann" . "par(\"ann\")")     ("axes" . "TRUE")    ("frame.plot" . "axes")    ("panel.first" . "NULL")    ("panel.last" . "NULL")    ("asp" . "NA")    ("..." . ""))
      ("x" "y" "..." "ci" "type" "xlab" "ylab" "ylim" "main" "ci.col" "ci.type" "max.mfrow" "ask" "mar" "oma" "mgp" "xpd" "cex.main" "verbose" "scale" "xlim" "log" "sub" "ann" "axes" "frame.plot"
       "panel.first" "panel.last" "asp" "center" "edge.root" "nodePar" "edgePar" "leaflab" "dLeaf" "xaxt" "yaxt" "horiz"
       "zero.line" "verticals" "col.01line" "pch" "legend.text" "formula" "data" "subset" "to" "from" "newpage" "vp" "labels"
       "hang" "freq" "density" "angle" "col" "border" "lty" "add" "predicted.values" "intervals" "separator" "col.predicted"
       "col.intervals" "col.separator" "lty.predicted" "lty.intervals" "lty.separator" "plot.type" "main2" "par.fit" "grid"
       "panel" "cex" "dimen" "abbrev" "which" "caption" "sub.caption" "id.n" "labels.id" "cex.id" "qqline" "cook.levels"
       "add.smooth" "label.pos" "cex.caption" "rows" "levels" "conf" "absVal" "ci.lty" "xval" "do.points" "col.points" "cex.points"
       "col.hor" "col.vert" "lwd" "set.pars" "range.bars" "col.range" "xy.labels" "xy.lines" "nc" "yax.flip" "mar.multi" "oma.multi")))
    ("print"
     (("base")
      (("x" . "")    ("digits" . "NULL")    ("quote" . "TRUE")    ("na.print" . "NULL")    ("print.gap" . "NULL")    ("right" . "FALSE")    ("max" . "NULL")    ("useSource" . "TRUE")    ("..." . ""))
      ("x" "..." "digits" "signif.stars" "intercept" "tol" "se" "sort" "verbose" "indent" "style" ".bibstyle" "prefix" "vsep" "minlevel" "quote" "right" "row.names" "max" "na.print" "print.gap"
       "useSource" "diag" "upper" "justify" "title" "max.levels" "width" "steps" "showEnv" "newpage" "vp" "cutoff" "max.level" "give.attr" "units" "abbrCollate" "print.x" "deparse" "locale" "symbolic.cor"
       "loadings" "zero.print" "calendar"))))
  "Alist of cached arguments for very time consuming functions.")


;;; HELP

(defun ess-r-get-object-help-string (sym)
  "Help string for ac."
  (let ((proc (ess-get-next-available-process)))
    (if (null proc)
        "No free ESS process found"
      (let ((buf (get-buffer-create " *ess-command-output*")))
        (when (string-match ":+\\(.*\\)" sym)
          (setq sym (match-string 1 sym)))
        (with-current-buffer (process-buffer proc)
          (ess-with-current-buffer buf
            (ess--flush-help-into-current-buffer sym nil t)))
        (with-current-buffer buf
          (ess-help-underline)
          (goto-char (point-min))
          (buffer-string))))))

(defun ess-r-get-arg-help-string (sym &optional proc)
  "Help string for ac."
  (setq sym (replace-regexp-in-string " *= *\\'" "" sym))
  (let ((proc (or proc (ess-get-next-available-process))))
    (if (null proc)
        "No free ESS process found"
      (let ((fun (car ess--funname.start)))
        (with-current-buffer (ess-command (format ".ess_arg_help('%s','%s')\n" sym fun)
                                          nil nil nil nil proc)
          (goto-char (point-min))
          (forward-line)
          (buffer-substring-no-properties (point) (point-max)))))))


;;; COMPANY
;;; http://company-mode.github.io/

(defun company-R-objects (command &optional arg &rest ignored)
  (interactive (list 'interactive))
  (cl-case command
    (interactive (company-begin-backend 'company-R-objects))
    (prefix (unless (ess-inside-string-or-comment-p)
              (let ((start (ess-symbol-start)))
                (when start
                  (buffer-substring-no-properties start (point))))))
    (candidates (let ((proc (ess-get-next-available-process)))
                  (when proc
                    (with-current-buffer (process-buffer proc)
                      (all-completions arg (ess--get-cached-completions arg))))))
    (doc-buffer (company-doc-buffer (ess-r-get-object-help-string arg)))))

(defun company-R-args (command &optional arg &rest ignored)
  (interactive (list 'interactive))
  (cl-case command
    (interactive (company-begin-backend 'company-R-args))
    (prefix (unless (ess-inside-string-or-comment-p)
              (let ((start (ess-arg-start)))
                (when start
                  (let ((prefix (buffer-substring-no-properties start (point))))
                    (if ess-company-arg-prefix-length
                        (cons prefix (>= (length prefix)
                                         ess-company-arg-prefix-length))
                      prefix))))))
    (candidates (let* ((proc (ess-get-next-available-process))
                       (args (delete "..." (nth 2 (ess-function-arguments
                                                   (car ess--funname.start) proc))))
                       (args (mapcar (lambda (a) (concat a ess-R-argument-suffix))
                                     args)))
                  (all-completions arg args)))
    (meta (let ((proc (ess-get-next-available-process)))
            (when (and proc
                       (with-current-buffer (process-buffer proc)
                         (not (file-remote-p default-directory))))
              ;; fixme: ideally meta should be fetched with args
              (let ((doc (ess-r-get-arg-help-string arg proc)))
                (replace-regexp-in-string "^ +\\| +$" ""
                                          (replace-regexp-in-string "[ \t\n]+" " " doc))))))
    (sorted t)
    (require-match 'never)
    (doc-buffer (company-doc-buffer (ess-r-get-arg-help-string arg)))))


;;; AC SOURCES
;;; http://cx4a.org/software/auto-complete/index.html

(defvar ac-source-R
  '((prefix     . ess-ac-start)
    ;; (requires   . 0) ::)
    (candidates . ess-ac-candidates)
    ;; (action  . ess-ac-action-args) ;; interfere with ac-fallback mechanism on RET (which is extremely annoing in inferior buffers)
    (document   . ess-ac-help))
  "Combined ad-completion source for R function arguments and R objects")

(defun ess-ac-start ()
  (when (ess-process-live-p)
    (or (ess-arg-start)
        (ess-symbol-start))))

(defun ess-ac-candidates ()
  "OBJECTS + ARGS"
  (let ((args (ess-ac-args)))
    ;; sort of intrusive but right
    (if (and ac-auto-start
             (< (length ac-prefix) ac-auto-start))
        args
      (if args
          (append args (ess-ac-objects t))
        (ess-ac-objects)))))

(defun ess-ac-help (sym)
  (if (string-match-p "= *\\'" sym)
      (ess-r-get-arg-help-string sym)
    (ess-r-get-object-help-string sym)))

;; OBJECTS
(defvar  ac-source-R-objects
  '((prefix     . ess-symbol-start)
    ;; (requires   . 2)
    (candidates . ess-ac-objects)
    (document   . ess-r-get-object-help-string))
  "Auto-completion source for R objects")

(defun ess-ac-objects (&optional no-kill)
  "Get all cached objects"
 (let ((aprf ac-prefix))
   (when (and aprf (ess-process-live-p))
     (unless no-kill ;; workaround
       (kill-local-variable 'ac-use-comphist))
     (ess--get-cached-completions aprf ac-point))))

;; ARGS
(defvar  ac-source-R-args
  '((prefix     . ess-arg-start)
    ;; (requires   . 0)
    (candidates . ess-ac-args)
    ;; (action     . ess-ac-action-args)
    (document   . ess-r-get-arg-help-string))
  "Auto-completion source for R function arguments")

(defun ess-ac-args ()
  "Get the args of the function when inside parentheses."
  (when  (and ess--funname.start ;; set in a call to ess-arg-start
              (ess-process-live-p))
    (let ((args (nth 2 (ess-function-arguments (car ess--funname.start)))))
      (if args
          (set (make-local-variable 'ac-use-comphist) nil)
        (kill-local-variable 'ac-use-comphist))
      (delete "..." args)
      (mapcar (lambda (a) (concat a ess-R-argument-suffix))
              args))))

(defvar ess--ac-help-arg-command
  "getArgHelp('%s','%s')")

(provide 'ess-r-completion)